[gmx-users] multiple peptides in the same box

[Justin Lemkul]

On 4/8/14, 10:17 PM, maggin wrote:
> Hi, everyone
>
> I want to put 12 peptides randomly in position and orientation in the same
> box. I'm not sure if the following is right, so I asked for help, please
> check if something wrong in it? Thank you very much for your kind help and
> suggestion !
>
> 1. pdb2gmx -f 1IYT.pdb -o 1IYT.gro -ignh -ter -water  spce  -ss  -p 1IYT.top
>
> 2. genconf -f 1IYT.gro -nbox 1 1 1  -o 1IYTlarge_box.gro -renumber -rot
> -maxrot 180 180 180
>
> 3. editconf -f 1IYTlarge_box.gro -o 1IYT_newbox.gro -c -d 1 -bt cubic
> -density 1000 -rotate 60 60 60
>
> 4. genbox -cp 1IYT_newbox.gro -nmol 11  -ci 1IYT_newbox.gro  -p topol.top
> -cs spc216.gro -o 1IYT_solv.gro
>
> At here, after delet  the #include "ffgromos43a1.itp" line, as well as all
> lines after the #endif line in the position restraint section. This includes
> any lines referring to spce.itp and ions.itp, as well as the [ system ] and
> [ molecules ] directives.
>
> I creat the top file, the content topol.top as follows:
>
> ; GROMACS topology
> ;
> ; Include the force field
> #include "gromos43a1.itp"
>
> ; Include chain topologies
> #include "topol_A.itp"
> #include "topol_B.itp"
> #include "topol_C.itp"
> #include "topol_D.itp"
> #include "topol_E.itp"
> #include "topol_F.itp"
> #include "topol_G.itp"
> #include "topol_H.itp"
> #include "topol_I.itp"
> #include "topol_J.itp"
> #include "topol_K.itp"
> #include "topol_L.itp"
>
> ; Include water topology
> #include "spce.itp"
>
> ; Include generic ion topology
> #include "ions.itp"
>
> [ system ]
> Twelve proteins in water
>
> [ molecules ]
> Protein_A	1
> Protein_B	1
> Protein_C	1
> Protein_D	1
> Protein_E	1
> Protein_F	1
> Protein_G	1
> Protein_H	1
> Protein_I	1
> Protein_J	1
> Protein_K	1
> Protein_L	1
>

Technically, there's nothing wrong with this, even if it is totally redundant. 
Twelve topologically identical proteins do not require separate .itp files.  All 
you need is:

[ molecules ]
Protein_A    12

As for the quality of the configuration, only you can judge whether it will be 
suitable for your purposes.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================